Federal employees are losing faith in their agency leaders, according to a new analysis from a nonprofit group.

Rank-and-file workers have never been wildly enthusiastic about the quality of leadership in their agencies, according to the Partnership for Public Service, which has compiled data on the best places to work in government since 2003. But in 2012, scores rating effective leadership dropped for the first time in nine years, a new study showed. Employees gave effective leadership a score of 52.8 out of 100 points in the Partnership’s 2012 survey, a decrease of 2.1 points from 2011. Still that’s higher than the 49.1 score employees gave effective leadership in 2003.

“Federal employees today are living in an environment of great uncertainty given budgetary constraints, pay freezes and staffing cutbacks, and at the same time feel less empowered to do their jobs and are less satisfied with the way their senior leaders are handling their agencies,” the analysis concluded.

Leadership scored lower than other issues, including pay, work-life balance and teamwork, according to the survey. Federal employees surveyed in 2012 who were planning to leave their jobs in the next year rated their agency 35 points lower in the effective leadership category than those staying in their positions. “This satisfaction gap between those planning to stay and those planning to leave was larger in leadership than any other workplace category,” stated the analysis, which the Partnership and Deloitte conducted, based on data from the Office of Personnel Management’s 2012 Federal Employee Viewpoint Survey. That survey and the Partnership’s annual Best Places to Work in the Federal Government study include feedback from hundreds of thousands of federal employees representing 362 agencies and subcomponents.

Within the effective leadership category, the survey solicited feedback from respondents in four sub-categories: empowerment, fairness, senior leaders and supervisors. Employees ranked empowerment at the bottom of the list, with a score of 45.8 points, while front-line supervisors fared the best out of the four sub-categories, garnering 62.3 points. “In each year of the Best Places to Work rankings between 2003 and 2012, federal employees gave their supervisors ratings that were more than 10 points above those of senior leaders,” the analysis stated. Even so, satisfaction with supervisors dropped 1.6 points from the 2011 score.

The federal government also continues to trail the private sector when it comes to effective leadership, the analysis found. Overall, federal employees gave their supervisors lower marks than did private sector workers, though both groups reported feeling less empowered in 2012 than in 2011. Government workers also believe they are not as well-informed as their private-sector counterparts: “The government lags behind the private sector by 17 points on employee satisfaction with the information they receive from management regarding what’s going on in their organization,” the survey said.

The trend isn’t all negative. For example, NASA, the State Department and the intelligence community improved their effective leadership scores in 2012, the Partnership found. The Transportation Department had the biggest increase, improving its 2012 score by 2.3 points. Employees ranked the departments of Agriculture, Homeland Security, Labor and Veterans Affairs lowest in the effective leadership category, with scores ranging from 45.7 points to 50.7 points.

The analysis recommended that senior leaders and managers engage with employees more often and in more substantive ways. “Find ways to let employees know they are valued, including getting to know them by walking the halls and listening to their concerns,” the study suggested. Other recommendations called on managers to conduct employee interviews and ask them about obstacles they face, offer timely and constructive feedback and communicate a clear leadership strategy through town halls, social media, and regular staff meetings, and develop “competency-driven executive coaching programs” to improve their own management skills.

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